Basically, if you're reading a JavaScript guide and it mentions document.write(), run away.
The MDC guides are much, much better. And Crockford's book is best.
There are also fantastic explanations of the Event model at PPK's Quirksmode site. Start here and read through all of his Event articles:
I also forgot GWT if you're coming from Java it could be a simple way to do some web development. I used it a bit at Seesmic and keep a good overall experience.
Of course GWT abstracts lot of things so you'll ended up by having a nice final product but not really understand the roots of html and javascript.
If you want to build plugins for your Framework of choice (JQuery in your case), then it is also a good idea to understand what is happening behind the scenes.
There are many situations where using a Framework is not really suited. Do you really need to embed your framework of choice (JQuery in your case) if the only thing you need is show or hide a single element of your page ?
I think "begin with a framework or not ?" is a long debate (whatever the language is). I don't have a good answer to this but in the long run knowing the language you use is recommended.
For HTML the w3schools guides are good http://www.w3schools.com/html/default.asp (the javascript one are also ok).
Once you get the basics of Javascript I'll recommend to go with one of this frameworks : JQuery, Prototype/scriptaculous, Mootools, Dojo, Google closure or Yahoo YUI.
There's no better ones, it's a matter of preference, I personally currently use JQuery but for some projects I used Mootools (great piece of code) and Prototype/scriptaculous. I heard a lot of goods for YUI also.